The Open Protein Structure Annotation Network
PDB Keyword


    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of hypothetical protein (np_356412.1) from Agrobacterium tumefaciens at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 1vqs Target Id 356437
    Molecular Characteristics
    Source Agrobacterium tumefaciens str. c58
    Alias Ids TPS1362,NP_356412.1 Molecular Weight 12168.54 Da.
    Residues 104 Isoelectric Point 6.74
    Sequence mfyeirtyrlkngaipaylkvvedegieiqkshlgelvgyffseigpineivhiwafsslddraerrar lmadprwlsflpkirdlievaenkimkparfsplm
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 5
    Resolution (Å) 1.50 Rfree 0.17681
    Matthews' coefficent 2.13 Rfactor 0.15099
    Waters 976 Solvent Content 41.69

    Ligand Information


    Google Scholar output for 1vqs
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
    2. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    3. A comparison of SAD and two-wavelength MAD phasing for radiation-damaged Se-MET crystals
    A Gonzlez - Journal of Synchrotron Radiation, 2006 - scripts.iucr.org
    4. Novel base triples in RNA structures revealed by graph theoretical searching methods
    M Firdaus-Raih, AM Harrison, P Willett - BMC , 2011 - biomedcentral.com
    5. Protein structural classification and family identification by multifractal analysis and wavelet spectrum
    SM Zhu, ZG Yu, A Vo - Chinese Physics B, 2011 - iopscience.iop.org

    Protein Summary

    The gene Atu4242 (AGR_L_1239) from Agrobacterium tumefaciens encodes the NP_356412 protein, a member of the NIPSNAP family PF07978. Genome context analysis provides several relevant hits (score above 0.9) with an aldehyde dehydrogenase (Atu4241) and an alkanal monooxygenase (AGR_L_1243).

    Another crystal structure of the protein from the same organism is available 2AP6.  1vqs belongs to the class of alpha and beta proteins and reveals a ferredoxin-like fold type SCOP54861, inside the NIPSNAP family. DALI top hit is with the Atu5224 protein PDB:1vqy (Z=19).  

    The NIPSNAP family proteins have putative roles in the vesicular transport [Ref].  Curiously, Agrobacterium tumefaciens seems to have an isoform NP_396154.1 of this protein with 51% sequence identity 1VQY.  Although, as individual subunits these proteins appear to be very similar, the protein encoded by  NP_396154.1, is perfectly organized into a volt-like superstructure.  In contrast, the product of NP_356412.1 seems to form simple homodimers.

    Ligand Summary





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